Service list

The German epigenome programme ‘DEEP’ is an interdisciplinary research network. Its goal is to generate data for biomedical interpretation of healthy and diseased cells. With this, DEEP will contribute to discover new functional epigenetic links useful for clinical diagnosis, therapy and health risk prevention. 

Prediction of protein sub-mitochondrial localization.

Prediction of secretory signal peptides and cleavage sites in proteins.

DELLY discovers germline and somatic structural variants in short-read massively parallel sequencing data

DESeq2 is an R/Bioconductor package for differential expression analysis of high-throughput sequencing assays (incl. RNA-seq, ChIP-Seq, 4C-Seq, ribosome profiling, CLIP, metagenomics, HT-CRISPR screens) based on the Gamma-Poisson distribution. Part of the Human Omics Analysis Toolbox

An R-package used to extract disease-perturbed subpathways within a pathway network as recorded by RNA-seq experiments.

DEXSeq is an extension of DESeq for the analysis of alternative exon usage. DESeq2 is an R/Bioconductor package for differential expression analysis of high-throughput sequencing assays (incl. RNA-seq, ChIP-Seq, 4C-Seq, ribosome profiling, CLIP, metagenomics, HT-CRISPR screens) based on the Gamma-Poisson distribution. Part of the Human Omics Analysis Toolbox

Database of human genes with their probability of being involved in a
hereditary disease (emerging service) 

OpenMS tool for targeted assay generation in metabolomics.

DIANA-LncBase provides an extensive collection of experimentally and on silico predicted miRNA:lncRNA interactions.

DIANA-microT web server is dedicated to miRNA target prediction and functional analysis and is widely used since 2009 from the scientific community. 

DIANA-mirExTra v2.0 performs a combined Differential Expression Analysis (DEA) of mRNAs and microRNAs (miRNAs) to uncover miRNAs and transcription factors (TFs) playing important regulatory roles between two investigated states.

DIANA-miRGen v3.0 provides accurate cell-line-specific miRNA gene transcription start sites (TSSs), coupled with genome-wide maps of transcription factor (TF) binding sites in order to unveil the mechanisms of miRNA transcription regulation.

DIANA-miRPath v3.0 is an online software suite dedicated to the assessment of miRNA regulatory roles and the identification of controlled pathways

OpenMS workflow for Data Independent Acquisition MS and statistical post-analysis.

Aan interactive, web-based exploratory data analytics application providing access to over 1,000 Dictyostelium gene expression experiments from Baylor College of Medicine.

We provide support and guidance in development of Disease Maps (disease-maps.org), computational and visual repositories of knowledge about mechanisms of human diseases. We offer hosting of open access Disease Maps on the MINERVA Platform (minerva-web.lcsb.uni.lu) on our infrastructure under the elixir-luxembourg.org sub-domain, their backup and conservation. The MINERVA Platform ensures online access, interactive exploration, search for known drug targets and visualisation of omics datasets. We provide training in management of the Disease Maps and guidance to their integration into reproducible computational workflows by using the dedicated API of the hosting platform.

A manually curated community resource annotating proteins for experimentally determined regions of intrinsic disorder from the literature.

Dissemination events: 

• Seminars / Webinars 
• Workshops
• Events for high-schools

Web interface for assignment and analysis of DNA conformers.

Online environment to learn to code based on automatic feedback on the submissions of programming exercises

DoGSite is a grid-based method which uses a Difference of Gaussian filter to detect potential protein binding pockets - solely based on the 3D structure of the macromolecules.

Database Of Local Biomolecumal COnfromers. (Formerly known as DOLCE)

Data, Otimization, Model and Evaluation: Recommendations for supervised machine learning validation in biology.

Dorothea contains human and mouse TF regulons. The human regulons were curated and collected from different types of evidence such as literature curated resources, ChIP-seq peaks, TF binding site motifs and interactions inferred directly from gene expression. The mouse regulons were constructed by mapping the human gene symbols to their orthologs in mice. Those regulons can be coupled with any statistical method that aims to analyse gene sets to infer TF activity from gene expression data. Preferably the statistical method viper is used.

This resource includes sequence pipeline (TarO) analysis, a secondary prediction (JPred) structure server, and a protein kinase database and kinase classification pipeline (Kinomer).

A bioinformatics tool for hypothesis generation and prioritization of drugs capable of modulating immune cell activity from transcriptomics data.

DSW@IFB is the support service for the development of data management plans in life sciences hosted by the French Bioinformatics Institute (IFB / ELIXIR-FR) and based an instance of the Data Stewardship Wizard<https://ds-wizard.org/>.

Tool to predict backbone dynamics from a single protein sequence

Plant Genomics and Phenomics Research Data Repository (e!DAL-PGP) is an infrastructure to comprehensively publish plant research data.